JP2016127844A - Selective lysis of cells - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide methods and devices for selectively lysing cells in a sample comprising micro-organisms such as bacteria in order to directly detect a pathogen in the sample such as whole blood, which contains a high amount of cellular material.SOLUTION: The invention relates to a method for detecting microorganisms in a sample comprising, in a blood sample with eukaryotic cells or the like containing or suspected to contain microorganisms and with a pH of about 9.5 or more, adding a nonionic surfactant and a buffer to the sample, incubating for a sufficient time to lyse eukaryotic cells, selectively lysing the eukaryotic cells, filtering and separating remaining microorganisms with a filter, lysing the microorganism, and performing nucleic acid based analysis; and to a device thereof.SELECTED DRAWING: Figure 1

Description

  The present invention relates to lysis of eukaryotic cells, and more specifically animal cells such as blood cells. The present invention further relates to the detection of microorganisms such as low concentrations of bacteria in samples containing high concentrations of other cells.

  Molecular diagnostics aims at fast detection of minute amounts of pathogens (typically bacteria) in samples such as blood. However, blood is a complex substrate, white blood cells (leukocytes) for the acquired immune system, red blood cells (erythrocytes) for the transmission of oxygen, and It comprises platelets (thrombocytes) for wound healing. This makes direct detection of pathogens in samples such as whole blood (containing large amounts of cellular material) difficult.

  Classical detection methods comprise the growth of bacteria in selective media and / or media with indicators. Typically, such an analysis requires at least one or two days of culture before performing the identification.

  In PCR-based methods, the amount of bacteria in a fresh blood sample is theoretically high enough to be detected without further culture of bacteria present in such samples. However, in order to detect a minute amount of bacteria at an early stage, a large amount of blood is required. Large amounts of DNA, especially in white blood cells, dramatically increase the background in DNA-based detection methods. In addition, the presence of hemoglobin-derived heme strongly reduces the activity of DNA polymerase. One microliter of human blood contains about 4,000 to 11,000 white blood cells and about 150,000 to 400,000 platelets. The DNA concentration in the blood is between 30-60 μg / mL. Detecting the presence of about 10-100,000 bacterial species in a 10 mL volume of whole blood is extremely challenging.

  Large amounts of leukocyte DNA can cause meaningless PCR products or can remove primers designed for the detection of bacterial DNA. This requires complete DNA purification and separation of mammalian DNA before detecting bacterial DNA by PCR or other methods.

  Apart from interfering with the PCR reaction itself, the amount of mammalian DNA increases the viscosity of the sample. In addition, lysed mammalian cell derived proteins and membranes form complexes that prevent sample filtration. This is particularly a problem for small devices. Further dilution of already large volumes of samples results in unacceptably long operating steps.

  For the above reasons, there is a need for a method for removing human DNA from a blood sample.

  Methods for specifically analyzing bacterial DNA in the presence of mammalian DNA are known. SIRSLab Looxter ™ uses a method of concentrating methylated DNA from a sample. Since bacterial DNA is highly methylated, this measure results in enrichment of bacterial DNA. Molzym's Polysis ™ uses a chaotropic agent and a surfactant to selectively lyse mammalian cells. This lysis step is followed by digestion with DNAse that is not affected by the chaotropic agent / surfactant. An alternative means marketed by Roche (Septifast ™) relies on PCR primer pairs specifically designed to prevent specific binding to and amplification of human DNA.

  US Pat. No. 6,803,208 discloses a method in which a suspension diluted with high-magnification platelets added with bacteria is lysed at 37 ° C. for 15 minutes (for visual inspection of bacteria retained on a filter thereafter). It is possible to filter a small amount of lysed sample with a 0.4 μm filter). However, this method cannot process large samples at room temperature.

BRIEF DESCRIPTION OF THE INVENTION

  Particular and preferred aspects of the invention are set out in the accompanying independent and cited claims. The specifics of a claim in a cited form may be combined with the specifics of a claim in an independent form and, with no particular limitation, the specifics of a claim in other appropriate forms specified in the claim .

  One aspect of the present invention relates to a method of selectively lysing eukaryotic cells, particularly animal cells, in a sample containing or suspected of containing microorganisms. This method comprises providing a sample with eukaryotic cells, in particular animal cells, including or suspected of containing microorganisms, adding a non-ionic detergent and buffer to the sample to a pH of about 9.5 or higher. And a step of incubating the solution for a sufficiently long time, eg, 30 seconds to 10 minutes, more preferably 2 to 6 minutes, to lyse eukaryotic cells, particularly animal cells. . In a specific embodiment, the dissolution can be performed at 15 to 30 ° C., more preferably near room temperature.

  In certain embodiments, the sample is a mammalian blood sample, such as whole blood.

  In other specific embodiments, the microorganism is a bacterium or a fungus.

  According to a particular embodiment, the ratio of the added surfactant and added buffer volume to the sample volume is 2/1 to 1/10.

  In a particular aspect, the nonionic surfactant is selected from the group consisting of Nonidet, Brij, Tween, Igepal, reduced triton, octyl glucoside, cholate and Triton. More preferred examples are Triton-X 100, Nonidet P40, sodium deoxycholate, and / or Igepal CA630.

  In a particular embodiment, the alkaline buffer used in the present invention has a pKa value greater than 9. Examples of the present invention include borate, carbonate, CAPS (N-cyclohexyl-3-aminopropanesulfonic acid), CAPSO (3- (cyclohexylamino) -2-hydroxy-1-propanesulfonic acid), CHES (2 -(N-cyclohexylamino) ethanesulfonic acid), pyrophosphoric acid and ethanolamine. A specific example is sodium carbonate. The buffer should have sufficient buffer capacity so that the final solution has a pH of about 9.5 or higher when mixed with the sample in the ratio of the present invention.

  In certain embodiments, the method filters the incubated solution with a filter having a pore size that retains the microorganisms on the filter, eg, a filter having a pore size of less than 0.7 μm, more preferably less than 0.5 μm. And further comprising a step. The method of the present invention facilitates filtration of large samples without enzymatic or heating related steps.

  In certain embodiments, the method further comprises the step of “neutralizing” after the selective lysis of the present invention to add an acid or acidic buffer to obtain a pH of about 7-9.

  In a particular embodiment, the method is followed by detection of microorganisms. Examples are cell counting, microscopy, PCR or culture.

  In certain embodiments, the method is followed by lysis of the microorganism.

  Another aspect of the present invention is an apparatus (1) for detecting microorganisms in a sample, the lysis chamber for receiving a volume of sample liquid of less than 40 mL, preferably less than 20 mL, more preferably 1-20 mL (2) a reservoir (3) connected to the lysis chamber, comprising an alkaline buffer having a pH of about 9.5 or higher and comprising a nonionic surfactant, or having a pH of about 9.5 or higher A reservoir (31) comprising an alkaline buffer, a reservoir (32) comprising a nonionic surfactant, a filter (4) connected to a lysis chamber for filtering the sample after lysis (where said The filter has a pore size that retains bacteria on the filter) and a detection chamber (5) for analyzing the presence of DNA On the device serving.

  In the present invention, the alkaline buffer typically has a pKa greater than 9.5, so the final solution will have a pH of about 9.5 or greater, and the nonionic surfactant is typically Are Triton X-100, sodium deoxycholate, Nonidet P40 and / or Igepal CA630.

  The method disclosed in the present invention allows the leukocytes and erythrocytes in the sample to be selectively lysed while the bacteria and fungi remain intact (whether dead or alive). .

  The method disclosed in the present invention makes it possible to process a sample without substantially diluting such a sample, and as a result, it is possible to process a larger amount of sample. In addition, for example, there is no need for enzymatic digestion of DNA with DNase or the use of heat, making this method less complex compared to methods known in the prior art.

  The method disclosed in the present invention produces a lysed sample with low viscosity and minimal agglomerates, allowing a large volume of lysed sample to be filtered through a filter that retains bacteria. Further processing of bacteria with such filters can proceed in volumes of about 100-1000 μL, fully automated in integrated cartridges, such as processing large amounts of signple in subsequent procedures, and neutralization and washing. It is possible to perform necessary operations.

  The above and other features, characteristics and advantages of the present invention will become apparent from the following detailed description when considered in conjunction with the accompanying drawings which illustrate, by way of example, the principles of the invention. This description is given for the sake of example only, without limiting the scope of the invention. The reference figures quoted below relate to the attached drawings.

FIG. 1 illustrates the filtration efficiency of large volumes of blood after selective dissolution at various pH values according to certain embodiments of the method of the present invention. FIG. 2 shows the recovery of various bacteria after lysis at various pH values according to certain embodiments of the method of the present invention. FIG. 3 shows the recovery of bacteria after lysis at various incubation times according to certain embodiments of the method of the present invention. FIG. 4 is a diagram showing reduction of human background DNA by selective lysis according to the present invention. FIG. 5 shows the detection of various types of pathogens in 1 mL of whole blood. FIG. 6 shows the detection of various types of pathogens in 5 mL of whole blood. FIG. 7 shows the difference between the manual method and the device method of the present invention. FIG. 8 is a diagram showing a comparison between a commercially available sepsis detection test and the method of the present invention. FIG. 9 shows pathogen lysis after selective lysis and capture on the filter of the present invention. FIG. 10 shows the pathogen lysis efficiency compared to other lysis methods when performed after the selective lysis and capture on the filter of the present invention. FIG. 11 shows a schematic overview of an embodiment of an apparatus for performing selective lysis as described in an embodiment of the present invention. FIG. 12 is a diagram illustrating an example of an integrated device comprising a selective lysis unit as described in aspects of the invention.

  In the various figures, the same reference signs refer to the same or analogous elements.

Detailed Description of the Invention

  The present invention will be described with respect to particular embodiments and with reference to certain drawings but the invention is not limited thereto but only by the claims. Any reference signs in the claims should not be construed as limiting the scope. The drawings described are only schematic and are non-limiting. In the drawings, the size of some of the elements may be exaggerated and not drawn on scale for illustrative purposes. Where the term “comprising” is used in the present description and claims, it does not exclude other elements or steps. Where a definite or indefinite article is used with reference to a singular noun, such as “a” or “an”, “the”, this includes the plural of that noun unless something else is specifically stated.

  Furthermore, the terms first, second, third, etc. in the specification and claims are used to distinguish between similar elements and necessarily mean a sequential or temporal order. It is not used to do. The terms so used are interchangeable under appropriate circumstances, and embodiments of the invention described herein operate in an order other than the order described or illustrated herein. It should be understood that it is also possible.

  The following terms or definitions are provided only to assist in understanding the present invention. These definitions should not be construed as having a narrower scope than would be understood by one skilled in the art.

Detailed Description of the Invention

  In the present invention, “blood cell” means a mammalian cell present in the blood, such as a red blood cell (erythrocyte), a white blood cell (leukocyte), and a platelet. (Thrombocytes).

  In the present invention, “whole blood” means untreated blood comprising plasma and blood cells and can be treated with an anticoagulant.

  “Sample” means an aqueous suspension comprising cellular material and containing bodily fluids such as lymph, cerebrospinal fluid, blood (whole blood and plasma), saliva, eg, muscle, brain Does not include the aqueous fraction of homogenized suspensions such as liver or other tissues.

  The “eukaryotic” of the present invention means any kind of eukaryotic organisms other than fungi such as animals, particularly animals including blood, and includes invertebrates such as crustaceans and vertebrates. Vertebrates comprise cold-blooded animals (fish, reptiles, amphibians) and warm-blooded animals (birds and mammals). Mammals specifically comprise primates, more specifically humans.

  As used herein, “selective lysis” refers to eukaryotics in which the percentage of microbial cells (such as bacterial cells) in a sample that are kept intact in the sample is kept intact in the organism from which the sample was collected. It is obtained when it is significantly higher (for example, 2, 5, 10, 20, 50, 100, 250, 500 or 1000 times or more) compared to the proportion of cells.

  “Microorganisms” as used in the present invention relate to bacteria (Gram positive and Gram negative bacteria and spore spores) and unicellular fungi such as yeast and mold, which are typically present as pathogens in the organism from which the sample was collected. To do.

  The first aspect of the present invention relates to a method of selectively lysing eukaryotic cells, particularly animal cells, in a sample containing or suspected of containing microorganisms such as bacteria. The aim of the method is to increase the sensitivity of the test to detect minute amounts of bacteria in a sample (ie, less than 10,000, less than 1000, less than 100 or less microorganisms in a 1 mL sample). As explained in the background of the present invention, the DNA of eukaryotic cells, particularly animal cells, in the sample interferes with PCR-based detection methods, and this DNA, together with proteins and membranes, is Aggregates are formed that increase viscosity and have a dramatic effect on the filtration of the lysed sample. In order to solve this problem, eukaryotic cells, especially animal cells, are selectively lysed, so that a substantial part of the microorganism (ie more than 20%, 40%, 60%, 80%, 90%, (Or even 95% or more) survive or contain bacterial DNA in the cell wall even if they die by the treatment. The method described in the present invention addresses the above problems.

  The method described in the present invention can be used, inter alia, for any type of sample in which the detection of microorganisms, in particular bacterial DNA, is inhibited by the presence of other cells containing DNA, in particular host cells in which the microorganism is present as a pathogen. It can also be applied to.

  The method described in the present invention is further illustrated for embodiments that test for the presence of minute amounts of bacteria in mammalian blood samples.

  The blood sample can be stored as whole blood or as a processed fraction such as a plasma or platelet preparation. Typically, the method described in the present invention is performed on freshly isolated whole blood. Such samples are generally treated with, for example, heparin, EDTA or citric acid to prevent condensation.

  Alternatively, the method is performed on fresh blood by collecting the blood directly from the vein into a tube with surfactant and buffer.

  Thus, fresh blood samples or stored samples are supplemented with buffers and non-ionic surfactants. Selection of the buffer and its concentration complements the buffer capacity of the blood sample and has a pH of about 9.5 or higher, more specifically 9.5 to 11.5, and even more specifically 9.5. Selected to obtain ~ 10.5. A pH value above 11.5 is suitable for more robust organisms such as gram positive bacteria and fungi. Similarly, the buffer may be added to the sample at a buffer volume of at most 200%, 150%, 100%, 50%, 20% or 10% of the sample volume to give the necessary change in pH. Fully concentrated.

  Buffers suitable in the present invention typically have a pKa greater than 9, greater than 9.5, and even greater than 10, borate, carbonate, CAPS, CAPSO, CHES, pyrophosphate, ethanolamine And other commonly used buffers having an optimum buffering capacity in the above pH range.

  Suitable surfactants are nonionic surfactants, which on the one hand have a lytic action only on eukaryotic cells, in particular animal cells, but on the other hand have a solubilizing action on DNA and proteins.

Examples of nonionic surfactants are alkali glycosides, Brij 35 (C12E23 polyoxyethylene glycol dodecyl ether) (15,7), Brij 58 (C16E20 polyoxyethylene glycol dodecyl ether (16), Genapol (13-19). , MEGA-8, -9, glucanid such -10, octyl glucoside _{(12,6), Pluronic F127, Triton} X-100 (C 14 H 22 O (C 2 H 4 O) n) (13,4), _{Triron X-114 (C 24 H} 42 O 6) (12,4), Tween20 ( polysorbate 20) (16,7) and Tween 80 (polysorbate 80) (15), Nonidet P40, sodium deoxycholate, reduced Triton X- 1 00 and / or Igepal CA630.
A particularly preferred example of a nonionic surfactant is Triton X-100.

  The most effective concentration of the surfactant varies depending on the surfactant, but is typically in the range of 0.1 to 5%, more specifically 0.1 to 1%. Depending on the surfactant (solid or liquid),% means w / v% or v / v%, respectively.

  Incubation of the blood sample in the presence of buffer and detergent is at a temperature of 10-30 ° C., more preferably near room temperature, within 10 minutes, preferably 30 seconds to 10 minutes, more preferably about 1 -3, 1-5, 1-8, 2-6 or 1-10 minutes.

  The process according to the invention has the advantage that selective dissolution is obtained within 10 minutes at a temperature of 30 ° C. or less. Thus, the method can generally be performed at ambient environmental temperatures without the need to heat the sample.

  After lysis, the pH of the lysed sample may be neutralized (ie, 7-9) by adding acid or acidic buffer in the neutralization step. At neutral pH, the lysed sample can be used for extended periods (up to 1 hour, 2 hours, 6 hours, 12 hours or even 24 hours without further lysis of the bacterial cells, without dramatic changes in the flow properties of the lysed sample Also) is known to be preserved.

  Another parameter investigated by the method of the present invention is an evaluation of the flow characteristics of the blood sample after lysis. This can be measured by confirming which volume of lysed blood can be filtered with a 0.22 μm filter. The method of the present invention allows the filtration of whole blood at least 2, 5, 7.5 or even 10 mL diluted by adding 1 volume of buffer / surfactant to 1 volume of sample.

  In general, the methods of the invention comprise the step of separating intact bacterial cells from a sample, typically performed by centrifugation or filtration. In certain embodiments, the intact bacteria typically have a pore size of less than 1 μm to retain bacteria having a size of 0.5-10 μm, such as commercially available filters with a pore size of 0.4 or 0.22 μm. The lysed sample is separated from the sample by passing it through a size filter. For sample filtration, there are various types of commercially available devices, such as filters adapted to fit the syringe, and after dissolution in the syringe, the liquid is filtered by manually applying pressure to the piston rod of the syringe. Pass through.

  Thereafter, the presence of bacteria (or fungi) on the filter can be examined. In certain embodiments, the presence of the microorganism is examined by PCR. For this purpose, the bacteria (or fungi) are washed out of the filter and further processed for PCR amplification. Alternatively, the filter is washed with lysis buffer to release the DNA from the microorganism and further used in the PCR reaction.

  Other detection steps can be performed by cell counting, microscopic observation, PCR or culture.

  Sample lysis, filtration and microbial detection can be performed in one apparatus (schematically depicted in FIG. 11). Accordingly, one aspect of the present invention is the apparatus (1), a lysis chamber (2) for receiving a sample solution having a volume of 1 to 10 mL, and the alkaline buffer solution connected to the lysis chamber (2). Or a reservoir (3) containing the surfactant, or a reservoir (31) containing the alkaline buffer and a reservoir (32) containing the surfactant. Within the device, the lysis chamber is connected to a filter (4) for filtering the lysed sample, whereby the microorganisms are retained on the filter. The apparatus further comprises a channel for removing microorganisms from the filter and lyses them in a separate chamber. Alternatively, the apparatus further comprises means for lysing the microorganisms on the filter, a channel for transferring lysed bacterial or fungal cell DNA from the filter to another chamber. The device may further comprise a DNA purification and detection chamber (5) for analyzing the presence of DNA. Typically, the detection chamber is a PCR module.

  An example of an apparatus in which selective lysis and subsequent DNA purification and identification is performed is depicted in FIG.

  Combinations of other systems and methods embodying the invention will be apparent to those skilled in the art.

  While preferred embodiments, specific structures and configurations and materials have been discussed herein for the apparatus of the present invention, various changes or modifications in form and detail may be made without departing from the scope and spirit of the invention. Can be broken.

Example 1
Effect of pH on Filtration The purpose of this experiment is to evaluate the effect of buffer pH on filtration efficiency. The buffering capacity was sufficient to obtain a similar pH in the final solution and was confirmed by measuring the pH of the final solution using conventional techniques known to those skilled in the art.

Buffer solution
-1M sodium borate, pH 9.0 + 1% Triton X-100
-1M sodium borate, pH 9.5 + 1% Triton X-100
-1M sodium carbonate, pH 10.0 + 1% Triton X-100
-1M sodium carbonate, pH 10.3 + 1% Triton X-100
-1M sodium carbonate, pH 10.8 + 1% Triton X-100
Included.

  1 mL of buffer was mixed with 1 mL of whole blood and incubated for 3 minutes. Thereafter, neutralization buffer was added and the mixture was filtered using a vacuum filtration facility with a size selective filter having a diameter of 25 mm and a pore size of 0.45 μm. The volume of blood that could pass through the filter until it was clogged was measured. The results are shown in FIG. This experiment shows that the final pH value should be around 9.5 or higher in order to obtain a sufficient amount of filtered blood for the analysis of low concentrations of pathogens.

Example 2
Figure 6 shows the effect of buffer pH on the recovery of intact pathogen ( E. coli ) after selective lysis of blood cells.

The buffer used was
-1M sodium borate, pH 9.0 + 1% Triton X-100
-1M sodium borate, pH 9.5 + 1% Triton X-100
-1M sodium carbonate, pH 10.0 + 1% Triton X-100
-1M sodium carbonate, pH 10.5 + 1% Triton X-100
Is included.

The same amount of bacteria was added to 1 mL of blood. This volume was treated with the above buffer for 3 minutes.
Thereafter, the blood was centrifuged (10 minutes, 4000 g) to recover intact bacteria. Bacteria were lysed using a standard alkaline lysis method and DNA was purified using a Qiagen spin mini kit. The amount of DNA was quantified using real-time PCR. The result is shown in FIG.

  The figure shows bacterial recovery as a function of the pH of the selective lysis buffer. At low pH values, leukocyte DNA is not degraded and inhibits the PCR reaction. At high pH values, bacteria begin to lyse during selective lysis and they are not recovered.

Example 3
Effect of incubation time on pathogen recovery This example demonstrates the effect of long-term incubation of blood with the selective lysis buffer of the present invention on the recovery of intact pathogens. A certain number of P. aeruginosa bacteria were added to the blood. 1 mL of sterilized blood was mixed with 1 mL of selective lysis buffer (1M sodium carbonate pH 10.0 + 1% Triton X-100) and incubated for 1, 2, 3, 5, 7, or 10 minutes. Then 1 mL of neutralization buffer was added. The pathogen was recovered by centrifugation (4000 g for 10 minutes) and the bacterial pellet was washed. Finally, the cells were lysed by a standard alkaline lysis method, followed by DNA purification using QiaAmp Blood mini kit. The recovered DNA amount was measured by real-time PCR. The results are shown in FIG. 3, indicating that the incubation is preferably performed for 30 seconds to 10 minutes.

Example 4
Reduction of human background by selective lysis according to the present invention Reduction of the amount of eukaryotic DNA of current methods, more specifically leukocyte DNA, if present, this is a subsequent measure for detection of pathogen DNA or RNA. This is important because it inhibits the PCR reaction. In order to examine the amount of residual background DNA, various blood samples were treated with the selective lysis protocol of the present invention, and the amount of leukocyte DNA during the PCR reaction was determined using RNase P detection kit (Applied Biosystems). And analyzed. The Ct values for these samples were compared to those obtained from a 200 μL whole blood sample (all leukocyte DNA present). In the literature, human DNA from 200 μL of whole blood is the maximum amount of background DNA that can be tolerated in a PCR reaction without inhibiting the amplification of pathogen DNA. The results of various PCR reactions are shown in FIG.

  This figure shows the difference in the amount of human background between a 1 mL blood sample (1M sodium carbonate pH 10.0 + 1% Triton X-100) treated according to the method of the present invention and a 200 μL whole blood reference sample. Various samples have been processed and PCR results are shown as individual data points. These results indicated that in the 1 mL sample treated according to the present invention, the amount of background DNA was much lower (higher Ct value) compared to the 200 μL whole blood reference sample. This result demonstrates that leukocyte DNA is effectively and fully removed from the sample using the method of the present invention.

Example 5
The purpose of this example is to demonstrate the detection of various types of pathogens from whole blood by using the method of the present invention. Various types of pathogens, gram negative ( P. aeruginosa ), gram positive ( S. aureus ) and fungus ( C. albicans ) were mixed together in 1 mL of blood. The blood sample is treated with selective lysis buffer (1 mL of 1 M sodium carbonate pH 10.0 + 1% TZ-100 solution) for 3 minutes, after which the pores are small enough to neutralize the pH and retain all cells. Filtered using a size selection filter. The filter was washed to remove residual inhibitors such as hemoglobin and leukocyte DNA. The cells were then lysed according to standard alkaline lysis protocols and the DNA was purified using Qiagen blood mini kit.

  Pathogen DNA was detected by real-time PCR; the Ct value is a measure of the amount of DNA. For quantification, a small portion of the sterilized blood sample was seeded on a blood agar plate to obtain a CFU count. The data shown in FIG. 5 shows that a small number of pathogens can be detected from whole blood. The reference sample contained the same number of bacteria directly lysed in a small volume of PBS buffer and then quantified using DNA purification and real-time PCR. Reference measurements and actual enrichment experiments from blood gave similar Ct values, thus demonstrating high recovery. Negative control (blood without bacteria) showed no PCR signal.

  This analysis makes it possible to use large amounts of blood. The experimental equipment was the same as in the above example, but the blood volume was increased to 5 mL. The reference sample contained the same number of pathogens as the 5 mL blood sample, but the cells were kept in a small amount of PBS and lysed directly. The result is shown in FIG.

  This experiment demonstrates the possibility of recovering a small number of pathogens from large amounts of blood. The data show that the concentration of recovered pathogen DNA is similar to the reference. It can therefore be concluded that during selective lysis, the majority of pathogens are intact and the reduction of leukocyte DNA is effective to prevent inhibition of pathogen PCR.

Example 6
The selective dissolution method of the present invention can be carried out in various ways, and is not particularly limited. However, the manual procedure and the procedure in which the method is performed by the apparatus of the present invention (integrated) Procedures). This embodiment compares such an integrated procedure with a manual procedure. The manual procedure requires manual pipetting, centrifugation, while the integrated procedure can perform all the necessary work using microfluidic cartridges and size selection filters. The basic biochemical protocol is similar: Selective lysis of leukocytes and erythrocytes using 1M sodium carbonate + 1% Triton X-100 solution is followed by a 3 min neutralization step. In the next step, the mixture is centrifuged (manual) or filtered (integrated), the cells are washed, and finally the DNA is released using standard alkaline lysis procedures. In the final step, the DNA is purified using Qiagen blood mini kit and detected by real-time PCR. The results of the integrated and manual procedures can be found in FIG. 7 below. Equivalent results are obtained, indicating that the results are independent of the analysis implementation format.

Example 7
In this example, the method of the present invention was evaluated against a commercially available method, that is, MolYsis Complete kit (manufactured by Molzym). This kit uses chaotropic agents and surfactants to selectively lyse mammalian cells. After this dissolution step, digestion with DNAse that is not affected by the chaotropic agent / surfactant is performed.

In this experiment, 1 mL blood samples were sterilized with various concentrations of S. aureus . One mL of blood was processed as described in Example 5 and another 1 mL was processed with MolYsis kit according to the manufacturer's instructions. Ct values are plotted in FIG. 8 against the concentration of cells, indicating that the method of the present invention is at least as efficient as the known MolYsis kit without the addition of enzymes or chaotropic salts.

Example 8
After selective lysis of blood cells and concentration of pathogen cells on a size selection filter, alkaline lysis is performed to achieve simultaneous lysis of the various pathogens on the filter, making the DNA available for PCR analysis.

FIG. 9 shows the results of the alkaline lysis procedure performed on the integrated cartridge. S. aureus of 10 ⁶ cells in 1mL of blood, P. aeruginosa and C. albicans was Kakin. After selective lysis of blood cells and concentration of the pathogen on the filter, alkaline lysis was performed by incubating with 200 μL of a solution containing 200 mM NaOH, 0.5% SDS at 95 ° C. for 10 minutes. Complete lysis of the pathogens was achieved. The eluate containing pathogen DNA was neutralized with 20 μL of 1 M citric acid solution and purified using QIAamp DNA / Blood Mini kit. As a control sample, each pathogen of 10 ⁶ cells was lysed on a bench, neutralized and purified as described above.

Candida albicans was chosen as a model system for optimization and comparative evaluation of the alkaline lysis procedure, because these yeast cells are difficult to lyse and are well known for their tight cell walls. FIG. 10 shows a procedure for alkaline lysis (using 50 mM NaOH, 0.25% SDS in combination with heat treatment) and other lysis methods, namely high intensity ultrasonic (HiFU) treatment and commercial kit (BD It is a figure which compares with GeneOhm lysis kit. For alkaline lysis and lysis with a commercial kit, samples were concentrated from 1 mL to 160 μL and 100 μL, respectively, using centrifugation. For HiFU, 2 mL of cell solution was used without prior concentration. After lysis, unlysed cells and debris were removed from the sample by centrifugation. 1 μL of crude lysate was used as input for PCR.

  The combination of NaOH and SDS was more effective for dissolution than each of the individual compounds. Increasing the concentration of either compound did not further increase dissolution efficiency. Alkaline lysis without a thermal incubation step is significantly less efficient. Although lysis efficiency can be increased by incubating at 95 ° C. for 2 minutes, longer incubation at 70 ° C. is preferred for integrating the analysis into the cartridge.

  For alkaline lysis, cells are resuspended in 100 μL of lysis solution containing 50 mM NaOH and 0.25% SDS. Subsequently, the sample was incubated at 70 ° C. for 10 minutes, rapidly cooled to room temperature, and neutralized by adding 30 μL of 500 mM Tris-HCl, pH 7.0 (final concentration 150 mM Tris, ie, three concentrations of NaOH). Get double).

  In crude lysate PCR, unlysed cells and debris were removed from the samples by centrifugation (5 minutes, 14,000 g). 1 μL of supernatant was added to a 25 μL PCR reaction. Detection by PCR was based on Taqman PCR analysis (manufactured by Apollo) targeting rRNA gene. PCR reactions were performed in Taqman Universal Mastermix (Applied Biosystems) using 500 nM forward primer and 300 nM reverse primer and FAM-BHQ1 labeled probe (all oligonucleotide customs were synthesized by Biolegio BV). went. The PCR reaction was performed in a Bio-Rad CFX real-time PCR system. After activating the hot start polymerase with an initial heating step at 95 ° C. for 10 minutes, 50 cycles of 95 ° C. for 15 seconds and 60 ° C. for 1 minute were used. The fluorescent signal was detected during the 60 ° C. step in each cycle. Data analysis was performed using CFD software from Biorad.

Claims (15)

A method of selectively lysing eukaryotic cells in a sample containing or suspected of containing a microorganism comprising:
a) providing a sample with eukaryotic cells containing or suspected of containing microorganisms;
b) adding a nonionic surfactant and a buffer to the sample to obtain a solution with a pH of around 9.5 or higher,
c) Incubating said solution for a length of time sufficient to lyse eukaryotic cells.   The method of claim 1, wherein the sample is a mammalian blood sample.   The method of claim 2, wherein the blood sample is whole blood.   The method according to any one of claims 1 to 3, wherein the microorganism is a bacterium.   The method according to any one of claims 1 to 3, wherein the microorganism is a fungus.   The method according to any one of claims 1 to 5, wherein step c) of the incubation is performed for 30 seconds to 10 minutes.   The method according to claim 1, wherein the ratio of the added surfactant and added buffer volume to the sample volume is 2/1 to 1/10.   8. A method according to any one of the preceding claims, wherein the nonionic surfactant is present at a concentration of 0.1 and 5% (w / v% or v / v%).   9. The method according to any one of claims 1 to 8, wherein the nonionic surfactant is selected from the group consisting of Noidet P40, deoxycholate, Igepal CA630 and / or Triton-X100.   The method according to any one of claims 1 to 9, further comprising centrifuging the incubated solution and isolating the microorganism.   11. The method according to any one of claims 1 to 10, further comprising the step of filtering the incubated solution with a filter having a pore size that retains microorganisms on the filter.   The method according to claim 1, further comprising a step of dissolving the microorganism.   13. A method according to any one of claims 1 to 12, further comprising nucleic acid based molecular analysis. An apparatus (1) for detecting microorganisms in a sample,
A dissolution chamber (2) for receiving a sample solution of less than 40 mL;
A reservoir (3) comprising an alkaline buffer with a pH of 9.5 or higher and a nonionic surfactant connected to a lysis chamber, or an alkaline buffer with a pH of about 9.5 or higher; A reservoir (31) comprising a liquid and a reservoir (32) comprising a nonionic surfactant,
A filter (4) connected to the lysis chamber for filtering the sample after lysis (wherein said filter has a pore size that holds the bacteria on the filter), and for analyzing the presence of DNA Detection chamber (5)
Comprising the device.   15. An apparatus according to claim 14, wherein the alkaline buffer has a pKa greater than 9.0 and the nonionic surfactant is Triton X-100.

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